For anyone who's ever wanted to explore an old wreck, maybe this is the next best thing. A new blog has just started up, detailing dive by dive the archaeological expedition at a wreck thought to be HMS Serapis. The Serapis was involved in one of the fiercest ship-to-ship battles of the American Revolution (pictured). On 23 September 1773 she engaged the US warship Bonhomme Richard in the North Sea, just off the coast of Yorkshire. The British had never been beaten in their home waters and called on the Bonhomme Richard to surrender but her captain, John Paul Jones, cried the now-famous words: "I have not yet begun to fight". He lashed the two ships together, which meant the Serapis couldn't aim her cannons at her opponent. The Bonhomme Richard sprayed the Serapis's deck with gunfire, and even though the US ship ended up sinking, Jones won the fight, and the British handed the Serapis over. She later ended up under the command of the French, who were US allies, and she sank off the coast of Madagascar in 1781, in a fire apparently started when a sailor dropped a lantern into a tub of brandy.

A historian and underwater archaeologist called Dick Swete spent years researching the battle and led a project which in 1999 discovered a wreck off Madagascar that's thought to be the Serapis. Unfortunately he died of malaria not long afterwards but the project continues and archaeologists are now exploring the wreck to confirm that it really is the Serapis and record everything they find. The divers are keeping a blog, and Mike Krivior described the first dive on 21 November. The wreck is about 22 metres down, and so far they've found glass bottles, ceramics, cannons, an anchor and copper sheathing around the hull - all in line with what you'd expect on an 18th-century ship. I'm fascinated by archaeology in general but there's something special about wrecks - I think it's because ships generally sink quite suddenly so you get a snapshot of all the details of daily life, one particular moment frozen in time for anything up to thousands of years. I'm looking forward to the next installment from the Serapis.

As promised a while ago, here's a short video I made of Michael Wright demonstrating his reconstruction of the Antikythera mechanism. I'm a journalist not a filmmaker, so please don't judge the quality too harshly! I hope though that this at least gives you a sense of what the Antikythera mechanism was, and what it could do. In all the research I did for Decoding the Heavens, nothing brought this incredible machine to life for me quite like sitting in Michael's workshop, sipping tea while watching those pointers dance gently round the zodiac...

This week's opening of the impressive Museum of Islamic Art in Doha, Qatar, has got a whole lot of press attention, with write-ups in the New York Times, Economist and elsewhere. The articles describe how the museum, paid for by the oil wealth of Qatar's ruling family, is housed in an elegant building designed by Chinese-born architect I.M. Pei, and contains a huge collection of exquisite art exhibits, from silk wall hangings to jade jewellery.

But they've all missed what I think is the most exciting exhibit of all: a manuscript by an 11th-century Andalusian engineer called al-Muradi. It is tantalisingly called The Book of Secrets about the Result of Thought, and it doesn't disappoint. In it, al-Muradi describes (and draws) more than 30 machines and devices, including war machines, calendars, the earliest Arabic description of water clocks, and complex mechanical figures called automata. His rugged clocks were driven by fast-moving streams and involved elaborate gear systems, sometimes lubricated by mercury - a feature not seen in Europe until the 13th century. Some included epicyclic gearing, in which small wheels are carried around on larger wheels. This is the earliest known description of such complex gearing apart from the Antikythera mechanism; this is a technique the Arabs may have learned from the Greeks, and then built on (for this reason al-Muradi gets a walk-on mention in Decoding the Heavens).

The Book of Secrets is normally held in the Biblioteca Medicea Laurenziana in Florence, but the Italians have lent it to the Qatar museum for a temporary exhibition that lasts until 22 February 2009. The manuscript has been badly defaced, but researchers at Leonardo L3 have spent months studying it using imaging techniques that they have developed to decode Renaissance manuscripts, and have read much more of the Book than has been possible before. They have produced an interactive digital version of the manuscript that is also being displayed in Qatar, along with physical models of two of al-Muradi's machines: The Clock with Three Characters and the excellently-named Fortress Demolisher.

According to Qatar newspaper The Peninsula, other scientific and mathematical manuscripts from the 11th to 15th centuries are also on display in Doha. Scholars from the Islamic world have been responsible for some fundamental scientific and technological advances, as well as preserving much ancient Greek knowledge that would otherwise have been lost. This is too little recognised, and I'm so pleased that the Qatar museum is showcasing Islamic science and technology as well as art.

PS I couldn't find any pictures from the Book of Secrets, so instead here's a picture of a water pump from The Book of Knowledge of Ingenious Mechanical Devices, written by the engineer al-Jazari in 1206.

Ancient civilisations have left some pretty amazing things for us to remember them by, from Stonehenge to the great pyramids of Egypt. But what will we be remembered for, thousands of years from now? The internet? The space station? The Large Hadron Collider? Not quite. According to a feature article in the December issue of Nature Reports Climate Change, our longest-lasting legacy is likely to be the carbon dioxide that we're pumping into the atmosphere.

According to Mason Inman, who wrote the article, most popular books and articles on climate change don't say much about the lifetime of carbon dioxide in the atmosphere, perhaps just saying "a century or more". But a group of climate scientists is now trying to spread the word that it will be much, much longer than that. Here's how University of Chicago oceanographer David Archer puts it in his book The Long Thaw:

"The climatic impacts of releasing fossil fuel CO2 to the atmosphere will last longer than Stonehenge. Longer than time capsules, longer than nuclear waste, far longer than the age of human civilisation so far."

He goes on to say that unless we kick our addiction to fossil fuels now, we could force the Earth out of its regular pattern of freezes and thaws - even delaying the next ice age by half a million years.

That's quite a legacy. But does it matter? Of course any change to the climate can have positive as well as negative effects. Unfortunately the predictions for global warming suggest that the planet won't just get gently warmer. As things heat up, it's likely that weather patterns will get more unstable, with more extreme events such as floods, droughts and storms. So while the greenhouse gases we produce will last, all kinds of other things, from glaciers to species to communities, may not. A friend of mine, science journalist Gaia Vince, is about to set off on a journey around the world, to see for herself how global warming is affecting the planet.

She says: "I never saw the dinosaurs, I missed the Mayan civilization - now is a uniquely fascinating time for all sorts of life on Earth and this is a chance to see it. It might be the last chance." She's keeping a blog, called Wandering Gaia, to tell the rest of us about what she finds.

There's a cute paper coming up in the journal Sleep Medicine about how the ancient Greeks and Romans explained dreams. It's by Joseph Barbera - no not the animator, but a sleep scientist based at the University of Toronto. He explains that the predominant view was that they were messages sent from the gods (although given the surreal nature of most dreams I can't imagine how this was anything other than totally confusing!) But this was also the first time that people started thinking about dreams in a more rational, naturalistic way. A philosopher called Democritus (460-370 BC), who came up with the excellent idea that everything in the universe is made up of tiny particles called atoms, thought that everything we perceive was due to fast-moving films of these atoms hitting our sensory organs. He figured that when they bypass the sensory organs and hit the soul directly, we dream.

The great philosopher Plato (427-347 BC) was one of the first to consider a psychological component to dreams. He said: "...in all of us, even the most highly respectable, there is a lawless wild beast nature, which peers out in sleep." In that respect, Plato wasn't so far from Freud's wish-fulfillment theory of dreaming, although Freud thought the wishes expressed in dreams are disguised, whereas Plato saw our desires as being played out more directly.

But out of all ancient scholars that we know about, Aristotle (384-322 BC) came up with the explanation that's closest to our understanding today. For him, dreams had no purpose. He firmly rejected the traditional view that dreams could foretell the future, arguing that if this appeared to happen it was just a coincidence. He saw wakefulness and sleep as characterised by the presence and absence of perception, respectively, and argued that we dream when the mechanism of perception is activated in the absence of external stimulation. He also said that the suspension of judgement in sleep causes us to accept the things we see in dreams as real. Barbera notes that this is supported by modern neuroimaging studies, which have shown that activity of the brain's frontal lobe is suppressed during REM sleep.

When I first started learning about Aristotle, I thought he was overrated. After all, he thought that the Earth was at the centre of the universe - a misconception that sent astronomy down the wrong path for centuries. But the more I read about him, the more I'm in awe of him. He didn't get everything right, but the insights he was able to gain about the world around him, in the absence of all the scientific evidence that we take for granted today, was so impressive. As Barbera points out, scientists weren't able to improve much on Aristotle's theory of dreams until the discovery of REM sleep in the 1950s. In that respect I guess he was further ahead of his time than even the Antikythera mechanism.

Copernicus is the guy who famously declared (much to the disgust of the Catholic church) that the Earth is not the centre of the universe, as it is orbiting the Sun. Other astronomers had suggested this before him, such as Aristarchus of Samos, an ancient Greek astronomer who lived in the third century BC. But the idea never caught on until Copernicus, and for that reason he's often described as "the father of modern astronomy".

People have apparently been looking for his tomb for a couple of centuries, and the latest search began in 2004, at the request of the local bishop. Scientists figured he was probably buried at Frombork Cathedral in northern Poland, because he served as a priest there. But there were hundreds of sets of remains under the cathedral's floor.

Eventually they found a likely candidate - the bones of a 70-year-old man (this is how old Copernicus was when he died). Forensic reconstruction of the skull showed that the man had a broken nose and a scar above his forehead - both features shown in a self-portrait of Copernicus as an old man. To clinch the case, researchers from Uppsala University in Sweden compared DNA from the skull with that from two strands of hair found inside a book that Copernicus owned (and now kept in a library at Uppsala University). They announced today that the two sets of DNA match.

I'm not sure what's happening to the bones - hopefully they'll be left under the floor so he can continue to rest in peace, though I guess he'll get a lot more visitors now. In his memory, here's a quote about Copernicus written by the all round literary genius Goethe:

"Of all discoveries and opinions, none may have exerted a greater effect on the human spirit than the doctrine of Copernicus. The world had scarcely become known as round and complete in itself when it was asked to waive the tremendous privilege of being the centre of the universe. Never, perhaps, was a greater demand made on mankind - for by this admission so many things vanished in mist and smoke! What became of our Eden, our world of innocence, piety and poetry; the testimony of the senses; the conviction of a poetic - religious faith? No wonder his contemporaries did not wish to let all this go and offered every possible resistance to a doctrine which in its converts authorized and demanded a freedom of view and greatness of thought so far unknown, indeed not even dreamed of."

Hurray, more mammoth news! Just a couple of weeks after scientists reported that it's possible to make clones from frozen corpses - raising the (faint) possibility of resurrecting extinct animals that have been preserved in the permafrost, a paper in Nature today reports the first genome sequence of a mammoth - in fact the first genome sequence of any extinct species.

The DNA comes from two woolly mammoths found frozen in Siberia, which lived 20,000 and 60,000 years ago. Stephan Schuster from Pennsylvania State University and his colleagues extracted DNA from the animals' hair, and were able to sequence 3.3 billion base pairs of DNA.

It's just a draft sequence so far, and only covers around 70% of the entire genome, but the researchers have some interesting results already. First, they estimate that the mammoth genome is about 4.7 billion base pairs long (about half as long again as the human genome). Second, by comparing the sequence to that of modern elephants they found that mammoths were evolving only half as fast as primates do. Third, they found that the mammoth genome differs from that of elephants by as little as 0.6% (that's about half the difference between humans and chimpanzees).

The researchers are particularly interested in identifying which of those differences are responsible for making a mammoth into a mammoth. They've found a few spots in the genome that seem to be unique to mammoths. But they'll need to do more research to prove that these changes really are responsible for particular mammoth characteristics. They also hope to investigate how mammoths adapted to cold climate, and why they became extinct.

Onto the really important question: can we use the genome sequence to bring mammoths back to life? Henry Nicholls (author of Lonesome George, a book about a Galapagos tortoise thought to be the last of his kind) has written a feature in the same issue of Nature about exactly this (though unfortunately you need a subscription to read it). Nicholls explains that to produce a living animal you need to master the following steps: create a virtually error-free genome sequence; synthesise a full set of chromosomes from these sequences; engulf them in a nuclear envelope; transfer that nucleus into an egg that would support it; and get that egg into a womb that would carry it to term.

Rather depressingly, none of these steps is currently possible. But the existence of close living relatives (ie elephants) would make the job a lot easier than for dinosaurs, say. And the science is progressing incredibly fast, even since the film Jurassic Park was released in 1993. Back then, the longest genome that had ever been sequenced was that of a virus. Even less than a decade ago, sequencing a mammalian genome was a years-long, multimillion-dollar project. Now it can be done by a single lab in just a few months.

The next genome sequence we're likely to see from an extinct species is that of our own closest relative, the Neanderthal, and after that maybe the cave bear. Unfortuanately dinosaur genomes (because dinos lived so much longer ago) are still well in the realm of science fiction.

[The image is of a slightly more artistic attempt to bring the mammoth to life - modern cave art by Birgit Hannwacker.]

Google Earth now includes a 3D reconstruction of ancient Rome. It's the first historical city to be added to Google Earth, and contains more than 6,700 buildings.

To create the virtual reality city, Google Earth teamed up with researchers from the Rome Reborn project at the University of Virginia. They have spent years building a digital model of Rome as it appeared in 320 AD. Their starting point was a 1:250 plaster model of the city called Plastico di Roma Antica, which is housed in Rome's Museum of Roman Civilisation.

You can see a tutorial on how to access Google's Rome here. To be honest I found it awkward to use, and not as impressive as it looks in this video. I really love this clip from the Rome Reborn project though, which flies you through the city's eerily empty streets. In 320 AD, Rome was home to a million people, and the capital of the western world. It's just so huge, and so incredibly grand. Of course the poverty that most of the city's inhabitants would have lived in doesn't show up well here. But leaving that to one side, you could almost believe that this was a vision of 1700 years in the future, not 1700 years in the past...

Well, it has been a good week for archaeology. First, researchers excavating the ancient Greek city of Himera in northern Sicily have unearthed the biggest necropolis found so far on the island, which they reckon could contain around 10,000 tombs. Most of the graves date from the 6th and 5th centuries BC, and among other things, researchers have found the skeletons of newborn babies, alongside the Greeks' version of babies' beakers - small terracotta vases complete with spouts. There's also a common grave containing a dozen young male skeletons, presumably soldiers, who had died violently, some with arrows still attached. I love that such significant finds are still emerging, along with such vivid insights into the way these people lived and died. Of course the tomb of Archimedes himself is somewhere on Sicily, still to be discovered. He was killed in 212 BC when the Romans attacked his home city of Syracuse. The Roman politician Cicero tracked the tomb down in 75 BC, and found it covered in brambles and thorns - he recognised it by a sphere and cylinder on top (put there to celebrate Archimedes' proof that the ratio of the volume of a sphere to the volume of the cylinder that contains it is 2:3). There have been plenty of modern attempts to find it, but no one has been able to track it down.

Meanwhile in Egypt they've found a new pyramid. It's the country's 118th so far, and it was buried in the sands at Saqqara (pictured), just south of Cairo. A 5-metre-high square base is all that's left, but when intact it was probably around 15 metres tall. The pyramid is around 4300 years old (makes the Antikythera mechanism seem so young!) and it probably belonged to the mother of King Teti, who was founder of Egypt's 6th Dynasty. Archaeologists hope to enter the burial chamber in the next couple of weeks, but unfortunately tomb raiders almost certainly looted any treasures there centuries ago (unlike the intriguing tomb of the Chinese Emperor Qin, which I wrote about yesterday). The BBC has a nice picture story about the newly-discovered pyramid, while USA Today's version gives more detail.

Finally, this blog post gives an extensive account of a talk given in Salisbury last week by Stonehenge researcher Mike Parker-Pearson. He was filling his audience in on a finding already covered by the BBC last month - that the stones of Stonehenge could be 500 years older than thought. At the site of old stone monument there's also a circle of 56 mysterious holes, called the Aubrey Holes after the guy who discovered them. These seem to be older than the actual megaliths themselves, dating from around 3000 BC, and there have been various theories about what they were for. Now Parker-Pearson has discovered compressed chalk at the bottom of one of them - evidence that it once held a stone. Rather than the huge stones being a late addition to the site, Parker-Pearson thinks it's likely that all of the Aubrey Holes held stones from the time they were dug, with cremated remains being buried under the stones.

From a huge necropolis to a pyramid to Stonehenge - all for honouring the dead. Makes modern-day graveyards look a bit paltry...

Part of the Terracotta Army of China's First Emperor goes on show at the High Museum of Art in Atlanta, Georgia, today. I was lucky enough to see the sell-out exhibit at the British Museum in London earlier this year, and I don't think I've ever experienced anything that brings the ancient past so vividly to life as these terracotta soldiers do.

They were built for Qin Shihuangdi, known as China's first emperor because he unified the country for the first time; he reigned from 221 to around 210 BC. The story of his terracotta army is world-famous - farmers digging a well in the outskirts of Xi'an in 1974 discovered the life-size figures buried in the ground. Archaeologists have since found around 8000 soldiers in a series of pits, standing in battle-ready formation to guard Qin's tomb.

The stunning thing is how detailed and individual the figures are - they were handmade with varying ages, hairstyles, uniforms and facial expressions. As well as soldiers there are officials, scribes, acrobats, strongmen (presumably Qin thought he would need entertaining as well as defending after his death), and horses with bronze chariots. In 2001 archaeologists discovered a diverted underground river, by which terracotta musicians played to lifesize bronze water birds.

But I think the most intriguing thing about the whole site is the Emperor's tomb itself. It has never been excavated, for fear that exposure to the air would damage the contents, so what's inside is a mystery. However we do have a description of the mausoleum written about a hundred years after Qin's death, by a historian called Sima Qian:

"As soon as the First Emperor became king of Chin [Qin], excavations and building had been started at Mount Li, while after he won the empire more than seven hundred thousand conscripts from all parts of the country worked there. They dug through three subterranean streams and poured molten copper for the outer coffin and the tomb was filled with models of palaces and pavilions and offices as well as fine vessels, precious stones and rarities. Artisans were ordered to fix up cross-bows so that any thief breaking in would be shot. All the country's streams, the Yellow River and the Yangtse were reproduced in quicksilver and by some mechanical means made to flow into a miniature ocean. The heavenly constellations were shown above and the regions of the earth below. The candles were made of whale oil to ensure their burning for the longest possible time."

It sounds like an Indiana Jones movie! Could this incredible description be accurate? Archaeologists have been using radar and other remote sensing techniques to try to glean what's inside. It's hard to get much information about this work, the results tend to come out as short statements from the official Chinese news agency, but I've gathered together what I could find.

There's definitely a huge underground palace inside the burial mound (see the second half of this news story). Qin's tomb is at the bottom, with symmetrical staircases leading down into the tomb, and wooden structures inside it. The tomb also has an effective drainage system, which has stopped groundwater seeping in.

Above this is a 30-metre high pyramid shaped chamber, with stepped walls, which archaeologists think could have been meant as a passageway for the Emperor's soul. Researchers believe there is a huge number of silver and bronze coins inside. And they have found a very high density of mercury in the soil, suggesting that the story about a quicksilver ocean could be true. There are some images here, but the paper is pretty technical.

One option to open the tomb without damaging the contents might be to seal off the whole site with a huge airtight tent. But apparently only one company in the world makes such tents, and they don't make them big enough. In 2007, Chinese archaeologists announced that they have no plans to excavate the tomb to see for sure what's inside.

According to China Daily, the deputy curator of the Terracotta Army, Cao Wei, said: "I would not witness the excavation in my life. In the foreseeable future the mausoleum will maintain the status quo."

I admire him for that. I completely agree that the tomb should not be opened unless researchers are certain that they can protect what's inside. But this is such a tantalising opportunity - unlike virtually all of the Egyptian pyramids, this site does not appear ever to have been ransacked by looters, and the riches and technology inside could be stunning. If I was in charge of the operation I don't know if I would have the patience to accept never knowing what it holds.